Generally speaking it doesn't make a difference. If it was a reward BOFF, like the Borg or Jem'Hadar, you want to keep those or have them train the officer you already have because of special abilities (like Torpedo Spread III). But, if you're leveling up and getting BOFFs from those missions it doesn't really matter- they practically come a dime a dozen- as long as they have the skills you want at the end of the day.
I use some to train my existing BOFFs in desired abilities.
Some BOFF come with interesting traits and might replace an existing BOFF.
Some BOFF get special treatment for special situations, ie. shuttle duty, or for beams, torps, mines, etc.
Some BOFF with mostly not that special abilities are hired to herd my tribbles, or to catering service (hold food and drink ready for the active officers).
Gold members got extra BOFF slots, and you gain some as you level up.